We share an open educational resource originally developed for postgraduate taught masters chemistry students at the University of Edinburgh to introduce the practical aspects of molecular dynamics simulations.
This course is designed for students with no prior experience in programming or computational chemistry. It is delivered over a month as a series of four 3-hour workshops in a computer-lab setting, with the final session dedicated to individual projects.
The course aims to equip students with practical skills necessary to perform meaningful molecular dynamics simulations, including:
- Using basic command-line interfaces;
- Navigating and utilising high-performance computing resources;
- Preparing, running, and troubleshooting molecular dynamics simulations using GROMACS software;
- Recognising the limitations of computational chemistry methods available;
- Applying these skills independently to real research systems.
The materials are openly shared via GitHub: https://github.com/Edinburgh-Chemistry-Teaching/MD_ResearchTechniques
The article sharing this material is currently under review in Journal of Open Source Education – please see CURRENT VERSION of the article.